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A new generation of pesticides is making honeybees far more susceptible to disease, even at tiny doses, and may be a clue to the mysterious colony collapse disorder that has devastated bees across the world, the US government's leading bee researcher has found. Yet the discovery has remained unpublished for nearly two years since it was made by the US Department of Agriculture's Bee Research Laboratory.

The release of such a finding from the American government's own bee lab would put a major question mark over the use of neonicotinoid insecticides – relatively new compounds which mimic the insect-killing properties of nicotine, and which are increasingly used on crops in the US, Britain and around the world.

Bayer, the German chemicals giant which developed theinsecticides and makes most of them, insists that they are safe for bees if used properly, but they have already been widely linked to bee mortality. The US findings raise questions about the substance used in the bee lab's experiment, imidacloprid, which was Bayer's top-selling insecticide in 2009, earning the company £510m. The worry is that neonicotinoids, which are neurotoxins – that is, they attack the central nervous system – are also "systemic", meaning they are taken up into every part of the plant which is treated with them, including the pollen and nectar. This means that bees and other pollinating insects can absorb them and carry them back to their hives or nests – even if they are not the insecticide's target species.

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In Britain, more than 1.4 million acres were treated with the chemical in 2008, as part of total neonicotinoid use of more than 2.5 million acres – about a quarter of Britain's arable cropland.

The American study, led by Dr Jeffrey Pettis, research leader at the US government bee lab in Beltsville, Maryland, has demonstrated that the insects' vulnerability to infection is increased by the presence of imidacloprid, even at the most microscopic doses. Dr Pettis and his team found that increased disease infection happened even when the levels of the insecticide were so tiny that they could not subsequently be detected in the bees, although the researchers knew that they had been dosed with it.

Dr Pettis told The Independent his research had now been put forward for publication. "[It] was completed almost two years ago but it has been too long in getting out," he said. "I have submitted my manuscript to a new journal but cannot give a publication date or share more of this with you at this time."

However, it is known about, because Dr Pettis and a member of his team, Dennis van Engelsdorp, of Penn State University – both leaders in research focusing on colony collapse disorder (CCD) – have spoken about it at some length in a film about bee deaths which has been shown widely in Europe, but not yet in Britain or the US – although it has been seen by The Independent.

In The Strange Disappearance of The Bees, made by the American film-maker Mark Daniels, Pettis and van Engelsdorp reveal that they exposed two groups of bees to the well-known bee disease nosema. One of the groups was also fed tiny doses of imidacloprid. There was a higher uptake of infection in the bees fed the insecticide, even though it could not subsequently be detected, which raises the possibility that such a phenomenon occurring in the wild might be simply undetectable.

Although the US study remains unpublished, it has been almost exactly replicated by French researchers at the National Institute for Agricultural Research in Avignon. They published their study in the journal Environmental Microbiology and said: "We demonstrated that the interaction between nosema and a neonicotinoid (imidacloprid) significantly weakened honeybees."

Neonicotinoids have attracted growing controversy since their introduction by Bayer in the 1990s, and have been blamed by some beekeepers and environmental campaigners as a potential cause of CCD, first observed in the US in 2006, in which billions of worker bees abruptly disappear from their hives.

Between 20 and 40 per cent of American hives have been affected, and CCD has since been observed in several other countries from France to Taiwan, though it has not yet been detected in Britain. Although Bayer insists its products are bee-safe, French and German beekeepers have blamed them for large bee losses. Neonicotinoids have been banned, to different degrees, in France, Germany, Italy and Slovenia, although they are freely sold and widely used in the US and Britain.

In the UK, the Co-op has banned them from farms from which it sources vegetables, but the Government has rejected appeals from beekeepers and environmentalists for their use to be suspended as a precaution. This week, however, an Early-Day Motion was tabled in the Commons by Martin Paton, the Labour MP for Gower, calling again for the Government to suspend use of the compounds following major new controversy in the US surrounding Bayer's latest neonicotinoid – clothianidin – which is increasingly being used in Britain. In November, a leaked internal document from the US Environmental Protection Agency showed that it was continuing to license clothianidin, even though its own scientists reported that the tests Bayer carried out to show the compound was safe were invalid.

Leading the calls for neonicotinoids to be banned in the Britain is Buglife, the invertebrate conservation charity, which last year published a review of all the research done on the chemicals' impact on "non-target" insects such as honeybees and other pollinators.

Yesterday the Buglife director, Matt Shardlow, said of the Pettis study: "This new research from America confirms that at very, very low concentrations neonicotinoid chemicals can make a honeybee vulnerable to fatal disease. If these pesticides are causing large numbers of honeybees, bumblebees, solitary bees, hoverflies and moths to get sick and die from diseases they would otherwise have survived, then neonicotinoid chemicals could be the main cause of both colony collapse disorder and the loss of wild pollinator populations.

"The weight of evidence against neonicotinoids is becoming irresistible – Government should act now to ban the risky uses of these toxins."

Bayer insists its neonicotinoids are safe for bees when used properly. Dr Julian Little, a spokesman for Bayer CropScience UK, said it was difficult for it to comment on an unpublished study. "It makes it impossible to look at their methods, it makes it impossible to check whether you can repeat the work, you don't know where they got the imidacloprid from, you don't know how they gave that to the bees," he said. But he added: "I'm sure there are some very interesting effects Dr Pettis has seen in a laboratory, but in reality, when you get to what's important to everybody, which is what happens in the field, you don't see these things happening. Bees are very, very important insects to Bayer CropScience and we recognise their importance."